title: Do amino acid biosynthetic costs constrain protein evolution in Saccharomyces cerevisiae?
abstract: Prokaryotic organisms preferentially utilize less energetically costly amino acids in highly expressed genes. Studies have shown that the proteome of Saccharomyces cerevisiae also exhibits this behavior, but only in broad terms. This study examines the question of metabolic efficiency as a proteome-shaping force at a finer scale, examining whether trends consistent with cost minimization as an evolutionary force are present independent of protein function and amino acid physicochemical property, and consistently with respect to amino acid biosynthetic costs. Inverse correlations between the average amino acid biosynthetic cost of the protein product and the levels of gene expression in S. cerevisiae are consistent with natural selection to minimize costs. There are, however, patterns of amino acid usage that raise questions about the strength (and possibly the universality) of this selective force in shaping S. cerevisiae's proteome.
authors.affiliation: Department of Computer Science and Engineering, Southern Methodist University, P.O. Box 750122, Dallas, TX 75275, USA. draiford@smu.edu
authors.forename: Douglas W
authors.initials: DW
authors.lastname: Raiford
authors.forename: Esley M
authors.initials: EM
authors.lastname: Heizer
authors.forename: Robert V
authors.initials: RV
authors.lastname: Miller
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Akashi
authors.forename: Michael L
authors.initials: ML
authors.lastname: Raymer
authors.forename: Dan E
authors.initials: DE
authors.lastname: Krane
mesh_terms: D000596:Amino Acids / Q000096:biosynthesis* / Q000737:chemistry; D000693:Anaerobiosis; D019143:Evolution, Molecular; D015966:Gene Expression Regulation, Fungal; D057927:Hydrophobic and Hydrophilic Interactions; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism*; D014867:Water / Q000737:chemistry
chemical_list: D000596:Amino Acids; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D014867:Water